[JAM1775]

Im trying to help so hopefully you can follow my twists and turns here because I often confuse myself !
But, I am confused why a street car carb would have square jets. I'd call your carb guy and ask about that. A Holley may normally come with ie: 72F/80R but the power valve in the front opens up at a given vacuum to equal approx. 8 jets...therefore square carb when you need the power. 72 +8 +80=160. If your carb was set as square all around at 71F/71R - 142 it would run very rough anywhere down low without an open throttle plate to compensate more air for the extra fuel. Unless, for some "custom" reason they put the PV in the rear ? Perhaps one of the race guys can qualify this but I thought a carb jetted dead square is usually for off the trailer WOT drag racing. Further, all motors being different but jetting for 392's we've seen in our area usually adds up to the 160-168 range for example , 74F/83R + the PV (8)= 165. I think a square setting of 71F/71R with no PV is very lean...the carb guy had to get you more fuel in the curve somehow in that custom build. If your carb guy put the PV in the rear no matter how good the carb/intake is that's still a very heavy dump (uneven 71+8) dump of fuel to the rear four cylinders. A carb can only equally atomize so much of a variance. Holley once told me 10-11 spread front/rear with the front having being the low yet having the extra fuel via the PV , to get closest to square jetting, would be about the biggest spread in main jets before one might have to go the xtra tuning level to adjusting air/fuel better using the air bleeds.
At the very least if YOU WERE square on all 4 the main jets you should then bump up front/rear equally. Better heads may want a bit more jet but 5 on one side is very heavy.

What bigger heads and intake might change is vacuum pull. With a normal carb again would be effect operation of the Power Valve which should be rated in the area of 1/2 your idle vacuum. Sorry for the rant but I think you DO have a Power Valve and your problem may simply be you need to install a lower or higher rated PV to give your motor that extra 1/2 second to rev and match with anticipated fuel dump from the PV. Two things...if you need a lower PV (your idle vacumm lessened) that means your carb is dumping fuel too early as vacuum drops fro your foot going down. The motor now needs to catch up.....dead spot then surge. OR...if your vacuum increased the motor might bog due to LACK OF FUEL until the vac drops lower to open the PV suddenly introduce a surge of fuel.

All you changed were heads and intake. In that regard I would normall expect a possibility of a slightly higher jet change and possible PV change. I'd call the carb guy and see if you can juts tune this out with one of those changes.